Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 1 of 145
Found at i:13 original size:8 final size:8
Alignment explanation
Indices: 1--63 Score: 87
Period size: 8 Copynumber: 8.2 Consensus size: 8
1 CTAAAACC
1 CTAAAACC
9 CTAAAACC
1 CTAAAACC
17 CTAAAACC
1 CTAAAACC
25 CT-AAACC
1 CTAAAACC
32 CTAAAACC
1 CTAAAACC
*
40 CT-GAACC
1 CTAAAACC
*
47 CT-GAACC
1 CTAAAACC
54 CTAAAACC
1 CTAAAACC
62 CT
1 CT
64 GAACCCTGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
7 20 0.39
8 31 0.61
ACGTcount: A:0.43, C:0.40, G:0.03, T:0.14
Consensus pattern (8 bp):
CTAAAACC
Found at i:32 original size:7 final size:7
Alignment explanation
Indices: 4--671 Score: 668
Period size: 7 Copynumber: 94.4 Consensus size: 7
1 CTA
4 AAACCCT
1 AAACCCT
11 AAAACCCT
1 -AAACCCT
19 AAAACCCT
1 -AAACCCT
27 AAACCCT
1 AAACCCT
34 AAAACCCT
1 -AAACCCT
*
42 GAACCCT
1 AAACCCT
*
49 GAACCCT
1 AAACCCT
56 AAAACCCT
1 -AAACCCT
*
64 GAACCCT
1 AAACCCT
*
71 GAACCCT
1 AAACCCT
*
78 GAACCCT
1 AAACCCT
*
85 GAACCC-
1 AAACCCT
*
91 GAACACCT
1 AAAC-CCT
*
99 GAACCCT
1 AAACCCT
*
106 GAACCCT
1 AAACCCT
*
113 GAACCCT
1 AAACCCT
*
120 GAACCCT
1 AAACCCT
*
127 GAACCCT
1 AAACCCT
*
134 GAACCCT
1 AAACCCT
*
141 GAACCCT
1 AAACCCT
*
148 GAACCCT
1 AAACCCT
*
155 GAACCCT
1 AAACCCT
*
162 GAACCCT
1 AAACCCT
*
169 GAACCCT
1 AAACCCT
*
176 GAACCCT
1 AAACCCT
*
183 GAACCCT
1 AAACCCT
*
190 GAACCCT
1 AAACCCT
*
197 GAACCCT
1 AAACCCT
*
204 GAACCCT
1 AAACCCT
*
211 GAACCCT
1 AAACCCT
*
218 GAACCCT
1 AAACCCT
*
225 GAACCCT
1 AAACCCT
*
232 GAACCCT
1 AAACCCT
*
239 GAACCCT
1 AAACCCT
*
246 GAACCCT
1 AAACCCT
*
253 GAACCCT
1 AAACCCT
*
260 GAACCCT
1 AAACCCT
*
267 GAACCCT
1 AAACCCT
*
274 GAACCCT
1 AAACCCT
*
281 GAACCCT
1 AAACCCT
*
288 GAACCCT
1 AAACCCT
*
295 GAACCCT
1 AAACCCT
*
302 GAACCCT
1 AAACCCT
*
309 GAACCCT
1 AAACCCT
*
316 GAACCCT
1 AAACCCT
*
323 GAACCCT
1 AAACCCT
*
330 GAACCCT
1 AAACCCT
337 AAAACCCT
1 -AAACCCT
345 AAACCCT
1 AAACCCT
352 AAAACCCT
1 -AAACCCT
360 AAACCCT
1 AAACCCT
367 AAACCCT
1 AAACCCT
374 AAACCCT
1 AAACCCT
381 AAACCCT
1 AAACCCT
388 AAACCCT
1 AAACCCT
395 AAACCCT
1 AAACCCT
402 AAACCCT
1 AAACCCT
409 AAACCCT
1 AAACCCT
416 AAACCCT
1 AAACCCT
423 AAACCCT
1 AAACCCT
430 AAACCCT
1 AAACCCT
437 AAACCCT
1 AAACCCT
444 AAACCCT
1 AAACCCT
451 AAACCCT
1 AAACCCT
458 AAACCCT
1 AAACCCT
465 AAACCCT
1 AAACCCT
472 AAACCCT
1 AAACCCT
479 AAACCCCT
1 AAA-CCCT
487 AAAACCCT
1 -AAACCCT
495 AAAACCCT
1 -AAACCCT
503 AAAACCCT
1 -AAACCCT
511 AAACCCT
1 AAACCCT
518 AAACCCT
1 AAACCCT
525 -AACCCT
1 AAACCCT
*
531 AACCCCT
1 AAACCCT
*
538 AACCCCT
1 AAACCCT
*
545 AACCCCT
1 AAACCCT
552 -AACCCT
1 AAACCCT
558 -AACCCT
1 AAACCCT
564 -AACCCT
1 AAACCCT
*
570 AACCCCT
1 AAACCCT
*
577 AACCCCT
1 AAACCCT
584 -AACCCT
1 AAACCCT
590 AAACCCCT
1 AAA-CCCT
598 -AACCCT
1 AAACCCT
604 AAAACCCT
1 -AAACCCT
612 AAACCCT
1 AAACCCT
619 AAACCCT
1 AAACCCT
* *
626 -GACCCC
1 AAACCCT
* *
632 AACCCCC
1 AAACCCT
*
639 AACCCCT
1 AAACCCT
*
646 AGACCCCT
1 A-AACCCT
654 AAAACCCT
1 -AAACCCT
*
662 AAATCCT
1 AAACCCT
669 AAA
1 AAA
672 NNNNNNNNNN
Statistics
Matches: 628, Mismatches: 15, Indels: 35
0.93 0.02 0.05
Matches are distributed among these distances:
6 40 0.06
7 494 0.79
8 90 0.14
9 4 0.01
ACGTcount: A:0.36, C:0.44, G:0.06, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:1102 original size:7 final size:7
Alignment explanation
Indices: 1087--1261 Score: 126
Period size: 7 Copynumber: 24.9 Consensus size: 7
1077 ATCCCTGAAT
1087 CCCTAAA
1 CCCTAAA
*
1094 CCTTAAA
1 CCCTAAA
1101 CCCTAAA
1 CCCTAAA
*
1108 CCCGAAA
1 CCCTAAA
*
1115 CCCCAAA
1 CCCTAAA
*
1122 CCCCTAAC
1 -CCCTAAA
*
1130 CCCTAAC
1 CCCTAAA
1137 CCCTAAA
1 CCCTAAA
1144 CCCCTAAA
1 -CCCTAAA
*
1152 CTCT-AA
1 CCCTAAA
1158 CCCTTAAA
1 CCC-TAAA
1166 CCCTAAA
1 CCCTAAA
*
1173 ACCT-AA
1 CCCTAAA
*
1179 CCC-AAT
1 CCCTAAA
1185 CCCT-AA
1 CCCTAAA
1191 CCCT-AA
1 CCCTAAA
1197 CCCTAAAA
1 CCCT-AAA
1205 CCCTAAA
1 CCCTAAA
1212 CCCTAAA
1 CCCTAAA
*
1219 CACCAAAAA
1 C-CC-TAAA
*
1228 CCTTAAA
1 CCCTAAA
*
1235 CGCTAAA
1 CCCTAAA
* *
1242 TCTTAAA
1 CCCTAAA
*
1249 ACCTAAA
1 CCCTAAA
*
1256 ACCTAA
1 CCCTAA
1262 GAATGGGATA
Statistics
Matches: 135, Mismatches: 23, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
6 23 0.17
7 82 0.61
8 26 0.19
9 4 0.03
ACGTcount: A:0.42, C:0.41, G:0.01, T:0.16
Consensus pattern (7 bp):
CCCTAAA
Found at i:1297 original size:32 final size:32
Alignment explanation
Indices: 1261--1335 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
1251 CTAAAACCTA
1261 AGAATGGGATAAATCCAAACCGGGATAACCGC
1 AGAATGGGATAAATCCAAACCGGGATAACCGC
* * *
1293 AGAATGGGATAAATCTAAACCGGGATATCCTC
1 AGAATGGGATAAATCCAAACCGGGATAACCGC
*
1325 CGAATGGGATA
1 AGAATGGGATA
1336 TCCCAACCTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (32 bp):
AGAATGGGATAAATCCAAACCGGGATAACCGC
Found at i:1546 original size:32 final size:32
Alignment explanation
Indices: 1501--1568 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
1491 CTAAGTATAA
*
1501 GATAATTCCAAACCGGGACAACCGCAGAATGG
1 GATAAATCCAAACCGGGACAACCGCAGAATGG
* * * * *
1533 GATAAATCTAAACCGGGATATCCTCCGAATGG
1 GATAAATCCAAACCGGGACAACCGCAGAATGG
1565 GATA
1 GATA
1569 TCCCTACCTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.18
Consensus pattern (32 bp):
GATAAATCCAAACCGGGACAACCGCAGAATGG
Found at i:1713 original size:235 final size:233
Alignment explanation
Indices: 1268--1726 Score: 756
Period size: 235 Copynumber: 2.0 Consensus size: 233
1258 CTAAGAATGG
*
1268 GATAAATCCAAACCGGGATAACCGCAGAATGGGATAAATCTAAACCGGGATATCCTCCGAATGGG
1 GATAAATCCAAACCGGGACAACCGCAGAATGGGATAAATCTAAACCGGGATATCCTCCGAATGGG
* * * * *
1333 ATATCCCAACCTGGAATAACTACGGTAGGTTCCCCGGTCTAAACTCGATAAAATGATGAACCGGT
66 ATATCCCAACCTGGAATAACTACGGCAGATTCCCCGGTCTAAACTCGAAAAAACGATGAACCGGA
* * * *
1398 GTCTAAACCATCTAAAACCGGCTATAGGATACTGAACCGGGACGGCATTTGAAAGGAATAACCGA
131 ATCTAAAACATCTAAAACCGGCTATAGGATACCGAACCGGGACGGCATTTAAAAGGAATAACCGA
*
1463 GGAATAGCGTAATCCAGGTTGGGATATCCTAAGTATAA
196 GGAAAAGCGTAATCCAGGTTGGGATATCCTAAGTATAA
*
1501 GATAATTCCAAACCGGGACAACCGCAGAATGGGATAAATCTAAACCGGGATATCCTCCGAATGGG
1 GATAAATCCAAACCGGGACAACCGCAGAATGGGATAAATCTAAACCGGGATATCCTCCGAATGGG
* *
1566 ATATCCCTACCTGGAATAACTACGGCAGATTACTTCCGGTCTAAACTCGAAAAAACGATGAACCG
66 ATATCCCAACCTGGAATAACTACGGCAGATT-C-CCCGGTCTAAACTCGAAAAAACGATGAACCG
1631 GAATCTAAAACATCTAAAACCGGCTATAGGATACCGAACCGGGACGGCATTTAAAAGGAATAACC
129 GAATCTAAAACATCTAAAACCGGCTATAGGATACCGAACCGGGACGGCATTTAAAAGGAATAACC
* *
1696 GGGGAAAAGCTTAATCCAGGTTGGGATATCC
194 GAGGAAAAGCGTAATCCAGGTTGGGATATCC
1727 CCGGGTTATC
Statistics
Matches: 208, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
233 91 0.44
234 1 0.00
235 116 0.56
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (233 bp):
GATAAATCCAAACCGGGACAACCGCAGAATGGGATAAATCTAAACCGGGATATCCTCCGAATGGG
ATATCCCAACCTGGAATAACTACGGCAGATTCCCCGGTCTAAACTCGAAAAAACGATGAACCGGA
ATCTAAAACATCTAAAACCGGCTATAGGATACCGAACCGGGACGGCATTTAAAAGGAATAACCGA
GGAAAAGCGTAATCCAGGTTGGGATATCCTAAGTATAA
Found at i:3017 original size:17 final size:17
Alignment explanation
Indices: 2991--3026 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2981 ACCTGAACTT
2991 ACTAACATTGTTAAAAA
1 ACTAACATTGTTAAAAA
*
3008 ACTAATATTGTTAAAAA
1 ACTAACATTGTTAAAAA
3025 AC
1 AC
3027 CGAAATCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.31
Consensus pattern (17 bp):
ACTAACATTGTTAAAAA
Found at i:3980 original size:19 final size:20
Alignment explanation
Indices: 3945--3992 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
3935 CAAACAACCC
*
3945 AAAACAGAAATGAATAAGCA
1 AAAACAAAAATGAATAAGCA
3965 AAAACAAAAATG-ATAAGCA
1 AAAACAAAAATGAATAAGCA
3984 AAAA-AAAAA
1 AAAACAAAAA
3993 ACACATAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 5 0.19
19 11 0.41
20 11 0.41
ACGTcount: A:0.73, C:0.08, G:0.10, T:0.08
Consensus pattern (20 bp):
AAAACAAAAATGAATAAGCA
Found at i:6838 original size:230 final size:229
Alignment explanation
Indices: 6430--6954 Score: 732
Period size: 230 Copynumber: 2.3 Consensus size: 229
6420 CATATTAGCA
* * *
6430 AAAAGAAGCATATGTCAACTAAAAACAGAGAGGAATAGTATTCTGCTAAGCAGAA-ATTACAAAA
1 AAAAGAAGAATATATCAACTAAAAACAGAGAGGAATAGTATTCTGCTCAGC-GAATATTACAAAA
* *
6494 ATATTATAAAGATACTATCCTGAGTTCTGAGAGCAAAGGAACTAGTGTAATGTTATTTGGAAAAT
65 ATATTATAAAGATACTATCCTCAGTTCTGAGAGCAAAGGAACTAGTGTAATGTTAATTGGAAAAT
* * **
6559 GAACTATAATGACAAAAATATAAATGATAAGCCGAAATCTAAGCGTGATTTGGGCCCAAAAAAAC
130 GAACTATAATGACAAAAATATAAATGAAAAGCCAAAATCTAAGCGTGATTCAGGCCCAAAAAAAC
*
6624 CAAACCACAAAATTATTCTACTAAGCAAAAACAAG
195 CAAACCACAAAATTACTCTACTAAGCAAAAACAAG
* * * *
6659 AAAAGAAGAATATATTAACTAAAAACAGAGAGGAAAATTATTCAGCTCAGCGAATATTACAAAAA
1 AAAAGAAGAATATATCAACTAAAAACAGAGAGGAATAGTATTCTGCTCAGCGAATATTACAAAAA
* * * * * * * *
6724 TCTTAATATAGATATTTTCTTCAG-TCTTGGGAGCAATGGAACTAGTGTCATGTTAATTGGAAAA
66 TATT-ATAAAGATACTATCCTCAGTTC-TGAGAGCAAAGGAACTAGTGTAATGTTAATTGGAAAA
* * * *
6788 -GTAACTATAATGACAAAAATATAAATGAAAAGCCAAAATCTAATCGTGATTCAGGCTCAGAAAC
129 TG-AACTATAATGACAAAAATATAAATGAAAAGCCAAAATCTAAGCGTGATTCAGGCCCAAAAAA
* *
6852 ACCAAACCCCAAAATTACTCTGCTAAGCAAAAACAAG
193 ACCAAACCACAAAATTACTCTACTAAGCAAAAACAAG
*
6889 AAAAGAAGAATATATCAACTAAAAACAGAGAGGAATAGTATTCTGCTCAGCGGATATTACAAAAA
1 AAAAGAAGAATATATCAACTAAAAACAGAGAGGAATAGTATTCTGCTCAGCGAATATTACAAAAA
6954 T
66 T
6955 TATTCTGCTA
Statistics
Matches: 259, Mismatches: 33, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
228 3 0.01
229 60 0.23
230 196 0.76
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (229 bp):
AAAAGAAGAATATATCAACTAAAAACAGAGAGGAATAGTATTCTGCTCAGCGAATATTACAAAAA
TATTATAAAGATACTATCCTCAGTTCTGAGAGCAAAGGAACTAGTGTAATGTTAATTGGAAAATG
AACTATAATGACAAAAATATAAATGAAAAGCCAAAATCTAAGCGTGATTCAGGCCCAAAAAAACC
AAACCACAAAATTACTCTACTAAGCAAAAACAAG
Found at i:15540 original size:21 final size:21
Alignment explanation
Indices: 15516--15586 Score: 142
Period size: 21 Copynumber: 3.4 Consensus size: 21
15506 ACAAAAAATT
15516 TGAACCGGACACTAAAACACC
1 TGAACCGGACACTAAAACACC
15537 TGAACCGGACACTAAAACACC
1 TGAACCGGACACTAAAACACC
15558 TGAACCGGACACTAAAACACC
1 TGAACCGGACACTAAAACACC
15579 TGAACCGG
1 TGAACCGG
15587 GACGGGATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.41, C:0.32, G:0.17, T:0.10
Consensus pattern (21 bp):
TGAACCGGACACTAAAACACC
Found at i:16611 original size:45 final size:44
Alignment explanation
Indices: 16556--16641 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 44
16546 TACATTCAAT
*
16556 ATCTTTACCTGATTCAAAC-CACCTAATCAAGCTTTATTACATACA
1 ATCTCTACCTGATTC-AACTCACCTAATCAAGCTTTA-TACATACA
*
16601 ATCTCTACCTGATTCAGCTCACCTAATCAAGCTTTATACAT
1 ATCTCTACCTGATTCAACTCACCTAATCAAGCTTTATACAT
16642 TAGGTCTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
44 7 0.18
45 31 0.82
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.34
Consensus pattern (44 bp):
ATCTCTACCTGATTCAACTCACCTAATCAAGCTTTATACATACA
Found at i:36459 original size:47 final size:47
Alignment explanation
Indices: 36390--36479 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 47
36380 AATACAGTTG
*
36390 CATACAATATATTTACCTGATTCAAAC-CACCTAATCAAGCTTTATTA
1 CATACAATATATCTACCTGATTC-AACTCACCTAATCAAGCTTTATTA
* *
36437 CATACAATATCTCTACCTGATTCAGCTCACCTAATCAAGCTTT
1 CATACAATATATCTACCTGATTCAACTCACCTAATCAAGCTTT
36480 GTACATTAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
46 2 0.05
47 37 0.95
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (47 bp):
CATACAATATATCTACCTGATTCAACTCACCTAATCAAGCTTTATTA
Found at i:37620 original size:16 final size:17
Alignment explanation
Indices: 37586--37621 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
37576 ACCACAAAAT
37586 ATTTGAAAGAACGTAAA
1 ATTTGAAAGAACGTAAA
*
37603 ATTTGAAAG-ACTTAAA
1 ATTTGAAAGAACGTAAA
37619 ATT
1 ATT
37622 AACTAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.31
Consensus pattern (17 bp):
ATTTGAAAGAACGTAAA
Found at i:41679 original size:36 final size:36
Alignment explanation
Indices: 41638--41800 Score: 179
Period size: 36 Copynumber: 4.3 Consensus size: 36
41628 GGTAGCTTTA
41638 GCTACACTTATCTGATCAAGTGACAAAA-TGATAAGT
1 GCTACACTTATCTGATCAAGTGA-AAAAGTGATAAGT
*
41674 GCTACACTTATCTGATCAAGAT-ACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAG-TGAAAAAGTGAT-A-----AG---T
41719 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
41756 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
41792 GGTA-ACTTA
1 GCTACACTTA
41801 GCTACACTTA
Statistics
Matches: 111, Mismatches: 3, Indels: 27
0.79 0.02 0.19
Matches are distributed among these distances:
35 8 0.07
36 64 0.58
37 3 0.03
40 2 0.02
42 2 0.02
45 3 0.03
46 29 0.26
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:41726 original size:46 final size:45
Alignment explanation
Indices: 41674--41835 Score: 186
Period size: 36 Copynumber: 3.8 Consensus size: 45
41664 AATGATAAGT
*
41674 GCTACACTTATCTGATCAAGAT-ACAAAGTGATAAGTGGTAGCTTTA
1 GCTACACTTATCTGATCAAG-TGAAAAAGTGATAAGTGGTAGC-TTA
41720 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG--T-
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTA
*
41756 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAACTTA
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTA
* *
41801 GCTACACTTATCTGATC-AGGGACAAA-TGATAAGTG
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTG
41836 ATCATACGTA
Statistics
Matches: 102, Mismatches: 4, Indels: 23
0.79 0.03 0.18
Matches are distributed among these distances:
36 32 0.31
37 2 0.02
40 2 0.02
42 1 0.01
43 9 0.09
44 8 0.08
45 19 0.19
46 29 0.28
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.28
Consensus pattern (45 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTA
Found at i:41752 original size:82 final size:81
Alignment explanation
Indices: 41614--41835 Score: 360
Period size: 82 Copynumber: 2.7 Consensus size: 81
41604 NNNNNNNNNN
41614 ACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAATGATAAGTGCTAC
1 ACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGA-AAAATGATAAGTGCTAC
41679 ACTTATCTGATCAAGAT-
65 ACTTATCTGATCAAG-TG
41696 ACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTAC
1 ACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAA-TGATAAGTGCTAC
41761 ACTTATCTGATCAAGTG
65 ACTTATCTGATCAAGTG
* * * *
41778 AAAAAGTGATAAGTGGTAAC-TTAGCTACACTTATCTGATC-AGGGACAAATGATAAGTG
1 ACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAATGATAAGTG
41836 ATCATACGTA
Statistics
Matches: 134, Mismatches: 4, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
79 9 0.07
80 7 0.05
81 25 0.19
82 93 0.69
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Consensus pattern (81 bp):
ACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAATGATAAGTGCTACA
CTTATCTGATCAAGTG
Found at i:43686 original size:167 final size:167
Alignment explanation
Indices: 43410--43743 Score: 643
Period size: 167 Copynumber: 2.0 Consensus size: 167
43400 GAGCTGCGTA
43410 TTGTAAAGAGTGACCTTATCCGTTACTTTGATAAGTGCGCCACAGAAGGATGTCCATGGCGTATT
1 TTGTAAAGAGTGACCTTATCCGTTACTTTGATAAGTGCGCCACAGAAGGATGTCCATGGCGTATT
43475 CGTGCAGTTAAGCTTCCCAATGCTCCAACTTTCACAATTAGAAGTCTTGAAGGAACACATACTTG
66 CGTGCAGTTAAGCTTCCCAATGCTCCAACTTTCACAATTAGAAGTCTTGAAGGAACACATACTTG
43540 TGGGAAAAATGCACAAAATGGGCACCATCAAGCTTCT
131 TGGGAAAAATGCACAAAATGGGCACCATCAAGCTTCT
*
43577 TTGTAAAAGAGTGA-CTTATCCGTTACTTTGCTAAGTGCGCCACAGAAGGATGTCCATGGCGTAT
1 TTGT-AAAGAGTGACCTTATCCGTTACTTTGATAAGTGCGCCACAGAAGGATGTCCATGGCGTAT
43641 TCGTGCAGTTAAGCTTCCCAATGCTCCAACTTTCACAATTAGAAGTCTTGAAGGAACACATACTT
65 TCGTGCAGTTAAGCTTCCCAATGCTCCAACTTTCACAATTAGAAGTCTTGAAGGAACACATACTT
43706 GTGGGAAAAATGCACAAAATGGGCACCATCAAGCTTCT
130 GTGGGAAAAATGCACAAAATGGGCACCATCAAGCTTCT
43744 ATGGATTGGA
Statistics
Matches: 165, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
167 156 0.95
168 9 0.05
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (167 bp):
TTGTAAAGAGTGACCTTATCCGTTACTTTGATAAGTGCGCCACAGAAGGATGTCCATGGCGTATT
CGTGCAGTTAAGCTTCCCAATGCTCCAACTTTCACAATTAGAAGTCTTGAAGGAACACATACTTG
TGGGAAAAATGCACAAAATGGGCACCATCAAGCTTCT
Found at i:45091 original size:4 final size:4
Alignment explanation
Indices: 45082--45122 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
45072 ATCTCCCTCA
45082 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
45123 ACTGGATTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:48053 original size:23 final size:24
Alignment explanation
Indices: 48022--48066 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
48012 TATTTCTTTT
*
48022 TTTATAAATAATTAATATTTATCG
1 TTTATAAATAATTAAAATTTATCG
*
48046 TTTA-AAATATTTAAAATTTAT
1 TTTATAAATAATTAAAATTTAT
48067 ATTTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTATAAATAATTAAAATTTATCG
Found at i:56992 original size:268 final size:261
Alignment explanation
Indices: 56504--57034 Score: 972
Period size: 268 Copynumber: 2.0 Consensus size: 261
56494 AGTTTAGTTG
56504 ATACATGGAAAAAAAGAGTTCAGGTTGAGTTGGATGCTAAATACGGTCCAAATCAGTCTGTTCCC
1 ATACATGGAAAAAAAGAGTTCAGGTTGAGTTGGATGCTAAATACGGTCCAAATCAGTCTGTTCCC
56569 TGGTCTGACGTTGCTAAATGTGGAATCAAGCACTATAGACCTTCTGAGGTGAAGAGTTCAGCAAC
66 TGGTCTGACGTTGCTAAATGTGGAATCAAGCACTATAGACCTTCTGAGGTGAAGAGTTCAGCAAC
*
56634 ACAATTCTCTGCAACTAAAACTGGTTTTGTTAAGCTTTTTCAAGGAGGGACTGGAACCAAGTCTG
131 ACAATTCTCTGCAACTAAAACTGGTTTTGTTAAGCTTTTTCAAGGAGGGACTGCAACCAAGTCTG
56699 CTTCTGCAATGCCGGTACCTATGAAGGCATCAACATTGCCTGCTTCAGCCAGAACAAAGGCGCGG
196 CTTCTGCAATGCCGGTACCTATGAAGGCATCAACATTGCCTGCTTCAGCCAGAACAAAGGCGCGG
56764 A
261 A
56765 ATACATGGAAAAAAAAGAGTTCAGGTTGAGTTGGATGCTAAATACGGTCCAAATCAGTCTGTTCC
1 ATACATGG-AAAAAAAGAGTTCAGGTTGAGTTGGATGCTAAATACGGTCCAAATCAGTCTGTTCC
*
56830 CTGGTCTGATGTTGCTAAATGTGGAATCAAGCACTATAGACCTTCTGAGGTTGCAGTGAAGAGTT
65 CTGGTCTGACGTTGCTAAATGTGGAATCAAGCACTATAGACCTTCTGA----G--GTGAAGAGTT
*
56895 CAGCAACACAATTCTCTGCAACTAAAATTGGTTTTGTTAAGCTTTTTCAAGGAGGGACTGCAACC
124 CAGCAACACAATTCTCTGCAACTAAAACTGGTTTTGTTAAGCTTTTTCAAGGAGGGACTGCAACC
56960 AAGTCTGCTTCTGCAATGCCGGTACCTATGAAGGCATCAACATTGCCTGCTTCAGCCAGAACAAA
189 AAGTCTGCTTCTGCAATGCCGGTACCTATGAAGGCATCAACATTGCCTGCTTCAGCCAGAACAAA
57025 GGCGCGGA
254 GGCGCGGA
57033 AT
1 AT
57035 GCTACTATTG
Statistics
Matches: 260, Mismatches: 3, Indels: 7
0.96 0.01 0.03
Matches are distributed among these distances:
261 8 0.03
262 103 0.40
266 1 0.00
268 148 0.57
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (261 bp):
ATACATGGAAAAAAAGAGTTCAGGTTGAGTTGGATGCTAAATACGGTCCAAATCAGTCTGTTCCC
TGGTCTGACGTTGCTAAATGTGGAATCAAGCACTATAGACCTTCTGAGGTGAAGAGTTCAGCAAC
ACAATTCTCTGCAACTAAAACTGGTTTTGTTAAGCTTTTTCAAGGAGGGACTGCAACCAAGTCTG
CTTCTGCAATGCCGGTACCTATGAAGGCATCAACATTGCCTGCTTCAGCCAGAACAAAGGCGCGG
A
Found at i:72829 original size:6 final size:6
Alignment explanation
Indices: 72820--72868 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
72810 TGGTCCTCAT
* * *
72820 CTCCAC CTCCAC CACCAC CTCCAC CTCCAA CTCCAC CTCCTC C-CCAC
1 CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC
72867 CT
1 CT
72869 TTCTTCAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
5 4 0.11
6 32 0.89
ACGTcount: A:0.18, C:0.65, G:0.00, T:0.16
Consensus pattern (6 bp):
CTCCAC
Found at i:75895 original size:2 final size:2
Alignment explanation
Indices: 75888--75918 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
75878 AATAAGGAAG
75888 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
75919 TGGTGAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:93058 original size:19 final size:19
Alignment explanation
Indices: 93018--93056 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
93008 TTTACTTCAC
93018 TTTCTTGTTTCTTTTCTTT
1 TTTCTTGTTTCTTTTCTTT
93037 TTTCTT-TTTCTTTT-TTT
1 TTTCTTGTTTCTTTTCTTT
93054 TTT
1 TTT
93057 TTTTTGGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 8 0.40
19 6 0.30
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (19 bp):
TTTCTTGTTTCTTTTCTTT
Found at i:96453 original size:26 final size:26
Alignment explanation
Indices: 96397--96453 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
96387 ACAAGTGGGA
*
96397 ATTTTAAGTAAAACGGAGAGTTTTGG
1 ATTTTAAGTAAAACGGAGAGTTTTGC
* * * * *
96423 GTTTTAAGTCATACGGGGCGTTTTGC
1 ATTTTAAGTAAAACGGAGAGTTTTGC
96449 ATTTT
1 ATTTT
96454 TGTTATAACT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.09, G:0.26, T:0.40
Consensus pattern (26 bp):
ATTTTAAGTAAAACGGAGAGTTTTGC
Found at i:101248 original size:26 final size:26
Alignment explanation
Indices: 101192--101248 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
101182 ACAAGTGGGA
*
101192 ATTTTAAGTAAAACGGAGAGTTTTGG
1 ATTTTAAGTAAAACGGAGAGTTTTGC
* * * * *
101218 GTTTTAAGTCATACGGGGCGTTTTGC
1 ATTTTAAGTAAAACGGAGAGTTTTGC
101244 ATTTT
1 ATTTT
101249 TGTTATAACT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.09, G:0.26, T:0.40
Consensus pattern (26 bp):
ATTTTAAGTAAAACGGAGAGTTTTGC
Found at i:104223 original size:22 final size:22
Alignment explanation
Indices: 104198--104254 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 22
104188 TCAATGGTTT
104198 ATTTTGCACACC-CTTAGTTTGC
1 ATTTTGCA-ACCACTTAGTTTGC
*
104220 ATTTTGCAACCAGTTTAGTTTGC
1 ATTTTGCAACCA-CTTAGTTTGC
104243 ATTTTGCAACCA
1 ATTTTGCAACCA
104255 GCTCAAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 3 0.09
22 8 0.25
23 21 0.66
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (22 bp):
ATTTTGCAACCACTTAGTTTGC
Found at i:104241 original size:23 final size:23
Alignment explanation
Indices: 104211--104255 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
104201 TTGCACACCC
104211 TTAGTTTGCATTTTGCAACCAGT
1 TTAGTTTGCATTTTGCAACCAGT
104234 TTAGTTTGCATTTTGCAACCAG
1 TTAGTTTGCATTTTGCAACCAG
104256 CTCAAAATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (23 bp):
TTAGTTTGCATTTTGCAACCAGT
Found at i:106355 original size:31 final size:31
Alignment explanation
Indices: 106317--106378 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
106307 TTTGTCTTTG
*
106317 TGCAAGATGTTTCTCTTTCAAAAAAAAAAAA
1 TGCAAGATGTTTCTCTGTCAAAAAAAAAAAA
106348 TGCAAGATGTTTCTCTGTCAAAAAAAAAAAA
1 TGCAAGATGTTTCTCTGTCAAAAAAAAAAAA
106379 CCTTAAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.27
Consensus pattern (31 bp):
TGCAAGATGTTTCTCTGTCAAAAAAAAAAAA
Found at i:107247 original size:93 final size:93
Alignment explanation
Indices: 107088--107738 Score: 1284
Period size: 93 Copynumber: 7.0 Consensus size: 93
107078 TCAAATGTAA
*
107088 ACAGCATATGTTAAGTCAAAATGGAACTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
1 ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
107153 TTAAGATTCATCAATTAAACAAAAATTC
66 TTAAGATTCATCAATTAAACAAAAATTC
107181 ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
1 ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
107246 TTAAGATTCATCAATTAAACAAAAATTC
66 TTAAGATTCATCAATTAAACAAAAATTC
107274 ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
1 ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
107339 TTAAGATTCATCAATTAAACAAAAATTC
66 TTAAGATTCATCAATTAAACAAAAATTC
107367 ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
1 ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
107432 TTAAGATTCATCAATTAAACAAAAATTC
66 TTAAGATTCATCAATTAAACAAAAATTC
107460 ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
1 ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
107525 TTAAGATTCATCAATTAAACAAAAATTC
66 TTAAGATTCATCAATTAAACAAAAATTC
107553 ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
1 ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
107618 TTAAGATTCATCAATTAAACAAAAATTC
66 TTAAGATTCATCAATTAAACAAAAATTC
107646 ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
1 ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
*
107711 TTGAGATTCATCAATTAAACAAAAATTC
66 TTAAGATTCATCAATTAAACAAAAATTC
107739 CAAGAAACTA
Statistics
Matches: 556, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 556 1.00
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (93 bp):
ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
TTAAGATTCATCAATTAAACAAAAATTC
Found at i:110319 original size:99 final size:100
Alignment explanation
Indices: 110189--110389 Score: 395
Period size: 99 Copynumber: 2.0 Consensus size: 100
110179 CCATTCGCGC
110189 GAGTTGCGCCTCCGCGCGCGCCTCGCCTTGTACCTGCAGCAACACACACAAACAGAAGAGCAAAA
1 GAGTTGCGCCTCCGCGCGCGCCTCGCCTTGTACCTGCAGCAACACACACAAACAGAAGAGCAAAA
110254 ATCGGGCCAACAAACAACAGAACAGATTTTTTTTA
66 ATCGGGCCAACAAACAACAGAACAGATTTTTTTTA
110289 GAGTTGCGCCT-CGCGCGCGCCTCGCCTTGTACCTGCAGCAACACACACAAACAGAAGAGCAAAA
1 GAGTTGCGCCTCCGCGCGCGCCTCGCCTTGTACCTGCAGCAACACACACAAACAGAAGAGCAAAA
110353 ATCGGGCCAACAAACAACAGAACAGATTTTTTTTA
66 ATCGGGCCAACAAACAACAGAACAGATTTTTTTTA
110388 GA
1 GA
110390 TTTTTTTTCT
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
99 90 0.89
100 11 0.11
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.17
Consensus pattern (100 bp):
GAGTTGCGCCTCCGCGCGCGCCTCGCCTTGTACCTGCAGCAACACACACAAACAGAAGAGCAAAA
ATCGGGCCAACAAACAACAGAACAGATTTTTTTTA
Found at i:110618 original size:10 final size:11
Alignment explanation
Indices: 110605--110634 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
110595 TTTTCATATG
110605 TTTTATTTTC-
1 TTTTATTTTCA
110615 TTTTATTTTCA
1 TTTTATTTTCA
110626 TTTTATTTT
1 TTTTATTTT
110635 GTTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:111270 original size:19 final size:19
Alignment explanation
Indices: 111248--111290 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
111238 CGCATATTTT
111248 TATATGTAATATATATATG
1 TATATGTAATATATATATG
* * * *
111267 TATATTTTATTTTTATATG
1 TATATGTAATATATATATG
111286 TATAT
1 TATAT
111291 AATTTTAAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (19 bp):
TATATGTAATATATATATG
Found at i:126032 original size:22 final size:22
Alignment explanation
Indices: 126005--126048 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
125995 TAGATAACTT
126005 TGTTGAAGATAAAATTTTAAAA
1 TGTTGAAGATAAAATTTTAAAA
126027 TGTTGAAGATAAAATTTTAAAA
1 TGTTGAAGATAAAATTTTAAAA
126049 GTCAATACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (22 bp):
TGTTGAAGATAAAATTTTAAAA
Found at i:127370 original size:27 final size:27
Alignment explanation
Indices: 127335--127387 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
127325 CATACAATAC
*
127335 AAAAAAATTAACAAATATTAATATATA
1 AAAAAAATTAACAAATACTAATATATA
127362 AAAAAAATTAACAAATACTAATATAT
1 AAAAAAATTAACAAATACTAATATAT
127388 GTTTGGTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (27 bp):
AAAAAAATTAACAAATACTAATATATA
Found at i:138183 original size:4 final size:4
Alignment explanation
Indices: 138170--138199 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
138160 AGTTGATGTT
138170 TTTC -TTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
138200 TTTTTTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:141018 original size:33 final size:33
Alignment explanation
Indices: 140976--141039 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
140966 TTTTATTTTG
140976 ACATTGTTTTGGACTGTAAATATGCTACTCTTA
1 ACATTGTTTTGGACTGTAAATATGCTACTCTTA
*
141009 ACATTGTTTTGGACTGTAAATATTCTACTCT
1 ACATTGTTTTGGACTGTAAATATGCTACTCT
141040 CTTTTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.44
Consensus pattern (33 bp):
ACATTGTTTTGGACTGTAAATATGCTACTCTTA
Found at i:144117 original size:13 final size:13
Alignment explanation
Indices: 144099--144127 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
144089 TTTCTTTGTG
144099 TTAAATTCACTAA
1 TTAAATTCACTAA
144112 TTAAATTCACTAA
1 TTAAATTCACTAA
144125 TTA
1 TTA
144128 GGATCCTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAATTCACTAA
Found at i:145344 original size:13 final size:14
Alignment explanation
Indices: 145318--145347 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
145308 GTATTCTTCC
145318 TTTATTTTTCCTCA
1 TTTATTTTTCCTCA
145332 TTTATTTTT-CTCA
1 TTTATTTTTCCTCA
145345 TTT
1 TTT
145348 CTTTATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATTTTTCCTCA
Found at i:159010 original size:5 final size:5
Alignment explanation
Indices: 159000--159024 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
158990 CTAACGTCAA
159000 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
159025 TTGCTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:177246 original size:21 final size:24
Alignment explanation
Indices: 177197--177246 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
177187 TATATTATAA
*
177197 TATATTTTTTAATTTTCACATTAT
1 TATATTTTTTAATATTCACATTAT
*
177221 AATATTTTTTAA-ATT-A-ATTAT
1 TATATTTTTTAATATTCACATTAT
177242 TATAT
1 TATAT
177247 AATATTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 9 0.39
22 1 0.04
23 2 0.09
24 11 0.48
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (24 bp):
TATATTTTTTAATATTCACATTAT
Found at i:177580 original size:3 final size:3
Alignment explanation
Indices: 177572--177622 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
177562 AGAACAAAAC
* * * *
177572 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCT TCG TCT TCA TCT TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
177620 TCA
1 TCA
177623 CCCAATTGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.25, C:0.33, G:0.02, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:189708 original size:7 final size:7
Alignment explanation
Indices: 189690--189723 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
189680 GCCTGCTGTG
189690 TATATG-
1 TATATGA
189696 TATATGA
1 TATATGA
189703 TATATGA
1 TATATGA
189710 TATATGA
1 TATATGA
189717 TATATGA
1 TATATGA
189724 ACATGGATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (7 bp):
TATATGA
Found at i:196253 original size:112 final size:113
Alignment explanation
Indices: 196113--196341 Score: 451
Period size: 112 Copynumber: 2.0 Consensus size: 113
196103 ATTAATTCAA
196113 TAATATTATTAATGACTAGTAAAAATTGAGTTATCATAAATAAATTTATATAAAAAGCGATTAAG
1 TAATATTATTAATGACTAGTAAAAATTGAGTTATCATAAATAAATTTATATAAAAAGCGATTAAG
196178 GGGAGCGTTAATATAATGATTTTTTTTATTAATAAAACATTTAATATT
66 GGGAGCGTTAATATAATGATTTTTTTTATTAATAAAACATTTAATATT
196226 TAATATTATTAATG-CTAGTAAAAATTGAGTTATCATAAATAAATTTATATAAAAAGCGATTAAG
1 TAATATTATTAATGACTAGTAAAAATTGAGTTATCATAAATAAATTTATATAAAAAGCGATTAAG
196290 GGGAGCGTTAATATAATGATTTTTTTTATTAATAAAACATTTAATATT
66 GGGAGCGTTAATATAATGATTTTTTTTATTAATAAAACATTTAATATT
196338 TAAT
1 TAAT
196342 TAAGTTTTTC
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
112 102 0.88
113 14 0.12
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.40
Consensus pattern (113 bp):
TAATATTATTAATGACTAGTAAAAATTGAGTTATCATAAATAAATTTATATAAAAAGCGATTAAG
GGGAGCGTTAATATAATGATTTTTTTTATTAATAAAACATTTAATATT
Found at i:204017 original size:15 final size:15
Alignment explanation
Indices: 203983--204017 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
203973 CCTCCATCCG
*
203983 GATCCCTCGCATTTA
1 GATCTCTCGCATTTA
*
203998 GATCTCTCGGATTTA
1 GATCTCTCGCATTTA
204013 GATCT
1 GATCT
204018 GACCATAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (15 bp):
GATCTCTCGCATTTA
Found at i:212082 original size:12 final size:12
Alignment explanation
Indices: 212065--212097 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
212055 ATGTTGAGAT
212065 ACAGAAGAAAAG
1 ACAGAAGAAAAG
212077 ACAGAAGAAAAG
1 ACAGAAGAAAAG
212089 ACAGAAGAA
1 ACAGAAGAA
212098 TTTTAAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.67, C:0.09, G:0.24, T:0.00
Consensus pattern (12 bp):
ACAGAAGAAAAG
Found at i:213019 original size:8 final size:8
Alignment explanation
Indices: 213006--213060 Score: 60
Period size: 8 Copynumber: 6.9 Consensus size: 8
212996 AAAAATTATT
213006 TTTATGTA
1 TTTATGTA
213014 TTTATGTA
1 TTTATGTA
*
213022 TTTATGATT
1 TTTATG-TA
213031 TTTAT-T-
1 TTTATGTA
*
213037 TTTATCTA
1 TTTATGTA
213045 TTTTATGTA
1 -TTTATGTA
213054 TTTATGT
1 TTTATGT
213061 GTATACATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 5 0.12
7 2 0.05
8 21 0.51
9 13 0.32
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.67
Consensus pattern (8 bp):
TTTATGTA
Found at i:213057 original size:23 final size:23
Alignment explanation
Indices: 213014--213058 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
213004 TTTTTATGTA
* *
213014 TTTATGTATTTATGATTTTTATT
1 TTTATCTATTTATGATATTTATT
213037 TTTATCTATTTTATG-TATTTAT
1 TTTATCTA-TTTATGATATTTAT
213059 GTGTATACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (23 bp):
TTTATCTATTTATGATATTTATT
Found at i:213284 original size:30 final size:28
Alignment explanation
Indices: 213250--213322 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
213240 AGCCAGTGCT
*
213250 CAAATAAAACAATTTTGAAGCA-TTAATAAC
1 CAAATAAAAC-ATTTT-AA-AATTTAATAAC
*
213280 CAAATTATAACATTTTAAAATTTAATAAC
1 CAAA-TAAAACATTTTAAAATTTAATAAC
213309 CAAAATAAAA-ATTT
1 C-AAATAAAACATTT
213323 AAGTATGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
28 5 0.14
29 15 0.41
30 12 0.32
31 5 0.14
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (28 bp):
CAAATAAAACATTTTAAAATTTAATAAC
Found at i:214181 original size:18 final size:18
Alignment explanation
Indices: 214158--214197 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
214148 TTATTATTTT
*
214158 TAAAATTT-ACTATTAAAA
1 TAAAATTTAAATATT-AAA
214176 TAAAATTTAAATATTAAA
1 TAAAATTTAAATATTAAA
214194 TAAA
1 TAAA
214198 TTATTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATTTAAATATTAAA
Found at i:214204 original size:19 final size:19
Alignment explanation
Indices: 214168--214218 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 19
214158 TAAAATTTAC
*
214168 TATTAAAATAAAAT-TTAAA
1 TATT-AAATAAATTATTAAA
214187 TATTAAATAAATTATTAAA
1 TATTAAATAAATTATTAAA
*
214206 -AAT-AATAAATTAT
1 TATTAAATAAATTAT
214219 ATTAATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 10 0.34
18 10 0.34
19 9 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTAAATAAATTATTAAA
Found at i:215272 original size:22 final size:22
Alignment explanation
Indices: 215247--215288 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
215237 TTTATAATTC
*
215247 AATCAATTGAATTAATTAAAAA
1 AATCAATTAAATTAATTAAAAA
* *
215269 AATCGATTAAATTCATTAAA
1 AATCAATTAAATTAATTAAA
215289 TTCGTATTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (22 bp):
AATCAATTAAATTAATTAAAAA
Found at i:236342 original size:31 final size:31
Alignment explanation
Indices: 236304--236364 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
236294 GATGCTTTTA
* *
236304 ATTTGACTATTAAGGCCTTTTTACCAAAAAT
1 ATTTGACTATTAAGGCCCTCTTACCAAAAAT
236335 ATTTGACTATTAAGGCCCTCTTACCAAAAA
1 ATTTGACTATTAAGGCCCTCTTACCAAAAA
236365 AAGTCCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (31 bp):
ATTTGACTATTAAGGCCCTCTTACCAAAAAT
Found at i:236926 original size:123 final size:122
Alignment explanation
Indices: 236714--236951 Score: 390
Period size: 123 Copynumber: 1.9 Consensus size: 122
236704 TTATTTCGAG
* **
236714 TTGACGTTTCTAGTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATCAGAGAAGAAATTGTG
1 TTGACGTTTCTAGTCAAATAGTATAAAATAGCTGATACCAGGATGCTATCAGAGAAGAAATTGTG
* *
236779 AAATCGTGCCCTCGTGGACGCGATTTCGGTACAGTTGGTCATGTAAGAAAAAAAAAT
66 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAAAAAAAAT
236836 TTGACGTTTTCTGAG-CAAATAGTATAAAATAGCTGATACCAGGATGCTAT-ATGAGAAGAAATT
1 TTGACG-TTTCT-AGTCAAATAGTATAAAATAGCTGATACCAGGATGCTATCA-GAGAAGAAATT
236899 GTGAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAA
63 GTGAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAA
236952 TAATTATTTT
Statistics
Matches: 108, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
122 7 0.06
123 99 0.92
124 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (122 bp):
TTGACGTTTCTAGTCAAATAGTATAAAATAGCTGATACCAGGATGCTATCAGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAAAAAAAAT
Found at i:240291 original size:22 final size:21
Alignment explanation
Indices: 240263--240313 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
240253 AAATATGGAT
*
240263 TTGAGAGATTTTTTGAAGGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
*
240285 TTGAGAGGATTTTGGAAGGAAT
1 TTGAGA-GATTTTGGAAGGAAA
240307 TTGAGAG
1 TTGAGAG
240314 TTTAAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:240711 original size:216 final size:216
Alignment explanation
Indices: 240337--240768 Score: 864
Period size: 216 Copynumber: 2.0 Consensus size: 216
240327 TGGAAGGAAA
240337 CAGAGAGAATATTTGTTTATGAAAAAATAAGGGGTAAGGGGTTTTATAGTAAAAAAAATTGTGAC
1 CAGAGAGAATATTTGTTTATGAAAAAATAAGGGGTAAGGGGTTTTATAGTAAAAAAAATTGTGAC
240402 CGTTGGGGGGGGCAACGGTCAAATTTTTTACTGTTGGGCCACTGTTCACGCGCGCGTGTCATCGC
66 CGTTGGGGGGGGCAACGGTCAAATTTTTTACTGTTGGGCCACTGTTCACGCGCGCGTGTCATCGC
240467 GTCCACGTCAGCGCGACCTGTTGACGTGGAAGGAAATCGCTTCCTTGAGGGCGCGATTGGCAGCG
131 GTCCACGTCAGCGCGACCTGTTGACGTGGAAGGAAATCGCTTCCTTGAGGGCGCGATTGGCAGCG
240532 ATTTCGCGGAATTGGCCCATT
196 ATTTCGCGGAATTGGCCCATT
240553 CAGAGAGAATATTTGTTTATGAAAAAATAAGGGGTAAGGGGTTTTATAGTAAAAAAAATTGTGAC
1 CAGAGAGAATATTTGTTTATGAAAAAATAAGGGGTAAGGGGTTTTATAGTAAAAAAAATTGTGAC
240618 CGTTGGGGGGGGCAACGGTCAAATTTTTTACTGTTGGGCCACTGTTCACGCGCGCGTGTCATCGC
66 CGTTGGGGGGGGCAACGGTCAAATTTTTTACTGTTGGGCCACTGTTCACGCGCGCGTGTCATCGC
240683 GTCCACGTCAGCGCGACCTGTTGACGTGGAAGGAAATCGCTTCCTTGAGGGCGCGATTGGCAGCG
131 GTCCACGTCAGCGCGACCTGTTGACGTGGAAGGAAATCGCTTCCTTGAGGGCGCGATTGGCAGCG
240748 ATTTCGCGGAATTGGCCCATT
196 ATTTCGCGGAATTGGCCCATT
240769 TCGGTAAATA
Statistics
Matches: 216, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
216 216 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.26
Consensus pattern (216 bp):
CAGAGAGAATATTTGTTTATGAAAAAATAAGGGGTAAGGGGTTTTATAGTAAAAAAAATTGTGAC
CGTTGGGGGGGGCAACGGTCAAATTTTTTACTGTTGGGCCACTGTTCACGCGCGCGTGTCATCGC
GTCCACGTCAGCGCGACCTGTTGACGTGGAAGGAAATCGCTTCCTTGAGGGCGCGATTGGCAGCG
ATTTCGCGGAATTGGCCCATT
Found at i:243781 original size:4 final size:4
Alignment explanation
Indices: 243774--243808 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
243764 AATGAATGAT
243774 TAAC TAAC TAAC TAAC -AGAC TAAC TAAC TAAC TAA
1 TAAC TAAC TAAC TAAC TA-AC TAAC TAAC TAAC TAA
243809 TATATCCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 1 0.03
4 27 0.93
5 1 0.03
ACGTcount: A:0.51, C:0.23, G:0.03, T:0.23
Consensus pattern (4 bp):
TAAC
Found at i:244237 original size:1 final size:1
Alignment explanation
Indices: 244231--244264 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
244221 TTTAAAACAT
244231 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
244265 CTGTTACTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:248321 original size:26 final size:26
Alignment explanation
Indices: 248292--248343 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
248282 GAGCCCCGCA
248292 TGAGCATCATTCCCACCAAAATCGTC
1 TGAGCATCATTCCCACCAAAATCGTC
248318 TGAGCATCATTCCCACCAAAATCGTC
1 TGAGCATCATTCCCACCAAAATCGTC
248344 ATTCAAGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.23
Consensus pattern (26 bp):
TGAGCATCATTCCCACCAAAATCGTC
Found at i:254218 original size:37 final size:35
Alignment explanation
Indices: 254143--254218 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
254133 ATCATTGTGC
* * *
254143 CTTCATGTATTTTGTTGTGTTACTCTTGATCGTGT
1 CTTCATGTAGTTTGTTGTGTTACCCTTGATCGTAT
*
254178 CTTCATGTAGTTTGTTGTGCATTACCCTTGATTGTAT
1 CTTCATGTAGTTTGTTGTG--TTACCCTTGATCGTAT
254215 CTTC
1 CTTC
254219 GTTAATCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 18 0.51
37 17 0.49
ACGTcount: A:0.13, C:0.17, G:0.18, T:0.51
Consensus pattern (35 bp):
CTTCATGTAGTTTGTTGTGTTACCCTTGATCGTAT
Found at i:257965 original size:25 final size:26
Alignment explanation
Indices: 257917--257965 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
257907 TTGGACTTAT
* * *
257917 TTGATCCTTTTTAATAGTATAGGGAA
1 TTGATCCTATTTAATAATAGAGGGAA
257943 TTGATCC-ATTTAATAATAGAGGG
1 TTGATCCTATTTAATAATAGAGGG
257966 GCCAATTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (26 bp):
TTGATCCTATTTAATAATAGAGGGAA
Found at i:260472 original size:72 final size:70
Alignment explanation
Indices: 260265--260548 Score: 383
Period size: 72 Copynumber: 4.0 Consensus size: 70
260255 ATATAGTATT
* * * * *
260265 TTAAACATGCAAAAAATTTAAAACTTTTTAAATTTATTTATACCAATTACACATTTAAAATATTT
1 TTAAACATGCAAAAAATTAAAAACTTATTAAATTTATTCATACCAATCACACATTTTAAATATTT
260330 ATATA
66 ATATA
* *
260335 TTAAATATGCAAAAAAATTAAAAAC--ATTAAATTTATTCATACCTATCACACATTTTAAATATT
1 TTAAACATGC-AAAAAATTAAAAACTTATTAAATTTATTCATACCAATCACACATTTTAAATATT
260398 TATATA
65 TATATA
* * *
260404 TTAAACATGCAAAAAATTAAAAAAACTTATTGAATTTATTCATACCAACCACACATTTTTAATAT
1 TTAAACATGCAAAAAATT--AAAAACTTATTAAATTTATTCATACCAATCACACATTTTAAATAT
260469 TTATATA
64 TTATATA
* * * *
260476 TTAAAAATACAAAAAAAATTAAAAACTTATTAAATTTATTCAAACCAAGCACACATTTTAAATAT
1 TTAAACATGC--AAAAAATTAAAAACTTATTAAATTTATTCATACCAATCACACATTTTAAATAT
260541 TTATATA
64 TTATATA
260548 T
1 T
260549 ACATACATAC
Statistics
Matches: 189, Mismatches: 18, Indels: 12
0.86 0.08 0.05
Matches are distributed among these distances:
68 8 0.04
69 48 0.25
70 15 0.08
71 13 0.07
72 97 0.51
74 8 0.04
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (70 bp):
TTAAACATGCAAAAAATTAAAAACTTATTAAATTTATTCATACCAATCACACATTTTAAATATTT
ATATA
Found at i:260627 original size:27 final size:27
Alignment explanation
Indices: 260589--260642 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
260579 ATACATCGAG
260589 ACCTTTGTTTCATGTTTAAAGTTTAAT
1 ACCTTTGTTTCATGTTTAAAGTTTAAT
260616 ACCTTTGTTTCATGTTTAAAGTTTAAT
1 ACCTTTGTTTCATGTTTAAAGTTTAAT
260643 GATGACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (27 bp):
ACCTTTGTTTCATGTTTAAAGTTTAAT
Found at i:261293 original size:23 final size:22
Alignment explanation
Indices: 261253--261303 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
261243 GATTTTTTTT
261253 TTTGTTAATATATCTTTTTAGTA
1 TTTGTTAATATATCTTTTTA-TA
* * * *
261276 TTTGTTAATGTTTTTTTTTATC
1 TTTGTTAATATATCTTTTTATA
261298 TTTGTT
1 TTTGTT
261304 TTTCCTCGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.18, C:0.04, G:0.10, T:0.69
Consensus pattern (22 bp):
TTTGTTAATATATCTTTTTATA
Found at i:266553 original size:31 final size:31
Alignment explanation
Indices: 266518--266582 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
266508 GAATTTTTTA
*
266518 AAAGGATAAACTTCAACTTGATTTAATCTAT
1 AAAGGATAAACTTCAACCTGATTTAATCTAT
*
266549 AAAGGATAAACTTTAACCTGATTTAATCTAT
1 AAAGGATAAACTTCAACCTGATTTAATCTAT
266580 AAA
1 AAA
266583 CACCTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (31 bp):
AAAGGATAAACTTCAACCTGATTTAATCTAT
Found at i:269603 original size:113 final size:113
Alignment explanation
Indices: 269302--269605 Score: 322
Period size: 112 Copynumber: 2.8 Consensus size: 113
269292 ACACAATTCA
* * *
269302 TTAACTTATCCAAAGTTCTATAAATATAAAATACCTTAAG--C----ACAATACGAGAAGATACA
1 TTAACTTATCAAAAGTTCTATAAACATAAAATACCGTAAGCACAATTACAATACGAGAAGATACA
* *
269361 CAAATACG-AAAAGAATACATGTATAACCAAATAAATCCAATACATTG
66 CAAATACGAAAAAGAATACATATATAACCAAATAAATCCAATACACTG
* * * * ** * *
269408 TTAACTTATCAAAAGTTCTATAAATATAAAATATCGTAAGTACGATTATTATACGAAAATATACA
1 TTAACTTATCAAAAGTTCTATAAACATAAAATACCGTAAGCACAATTACAATACGAGAAGATACA
* *
269473 CAAATAC-AAGAAGAATACATATATAAACCAAGTAAATCCAAT-CGACTG
66 CAAATACGAAAAAGAATACATATAT-AACCAAATAAATCCAATAC-ACTG
* * * * * *
269521 TTAACTTATCAAAAGTTGTA-AAACATAGAATACCTTAAGCGCAATTACAACACGAGAAGATGCA
1 TTAACTTATCAAAAGTTCTATAAACATAAAATACCGTAAGCACAATTACAATACGAGAAGATACA
*
269585 CAAATACGAAAAACAATACAT
66 CAAATACGAAAAAGAATACAT
269606 GATAAGTTCT
Statistics
Matches: 161, Mismatches: 27, Indels: 13
0.80 0.13 0.06
Matches are distributed among these distances:
106 37 0.23
108 1 0.01
112 74 0.46
113 49 0.30
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.25
Consensus pattern (113 bp):
TTAACTTATCAAAAGTTCTATAAACATAAAATACCGTAAGCACAATTACAATACGAGAAGATACA
CAAATACGAAAAAGAATACATATATAACCAAATAAATCCAATACACTG
Found at i:273247 original size:25 final size:25
Alignment explanation
Indices: 273213--273324 Score: 215
Period size: 25 Copynumber: 4.5 Consensus size: 25
273203 GTGCAAGACC
*
273213 AATTTTTAACCGTAGAAATGAGTGA
1 AATTTTTAACAGTAGAAATGAGTGA
273238 AATTTTTAACAGTAGAAATGAGTGA
1 AATTTTTAACAGTAGAAATGAGTGA
273263 AATTTTTAACAGTAGAAATGAGTGA
1 AATTTTTAACAGTAGAAATGAGTGA
273288 AATTTTTAACAGTAGAAATGAGTGA
1 AATTTTTAACAGTAGAAATGAGTGA
273313 AATTTTTAACAG
1 AATTTTTAACAG
273325 AAGGATCAGG
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
25 86 1.00
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (25 bp):
AATTTTTAACAGTAGAAATGAGTGA
Found at i:274199 original size:21 final size:22
Alignment explanation
Indices: 274166--274208 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
274156 TAATTATTTA
*
274166 AAACATATTTTTAATATATAAT
1 AAACATATATTTAATATATAAT
*
274188 AAACAT-TATTTAATATTTAAT
1 AAACATATATTTAATATATAAT
274209 GATTTAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (22 bp):
AAACATATATTTAATATATAAT
Found at i:288989 original size:21 final size:21
Alignment explanation
Indices: 288965--289044 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
288955 TAAGATCTTG
* *
288965 AATTTAATGTGAAATTGATCA
1 AATTTTATGCGAAATTGATCA
* * *
288986 AATTTTAT-TG-ATTTG-T-T
1 AATTTTATGCGAAATTGATCA
289003 AATTTTATGCGAAATTGATCA
1 AATTTTATGCGAAATTGATCA
*
289024 AATTCTATGCGAAATTGATCA
1 AATTTTATGCGAAATTGATCA
289045 TGAATTCGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
17 8 0.17
18 2 0.04
19 8 0.17
20 3 0.06
21 27 0.56
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.42
Consensus pattern (21 bp):
AATTTTATGCGAAATTGATCA
Found at i:302749 original size:4 final size:4
Alignment explanation
Indices: 302740--302770 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
302730 ATGTATAATA
*
302740 ATTT ATTT ATTT GTTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT
302771 AATATAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:306691 original size:18 final size:18
Alignment explanation
Indices: 306668--306702 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
306658 ATTAAAGCTG
306668 TGTATAATAAA-ATTAAAA
1 TGTATAA-AAATATTAAAA
306686 TGTATAAAAATATTAAA
1 TGTATAAAAATATTAAA
306703 TAAAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
TGTATAAAAATATTAAAA
Found at i:318527 original size:15 final size:15
Alignment explanation
Indices: 318507--318557 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
318497 TGGAATGGGA
318507 TATCCCCGACCGGCG
1 TATCCCCGACCGGCG
*
318522 TATCCCGCGA-TGG-G
1 TATCCC-CGACCGGCG
318536 ATATCCCCGACCGGCG
1 -TATCCCCGACCGGCG
318552 TATCCC
1 TATCCC
318558 GCGATGGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 4 0.13
15 22 0.73
16 4 0.13
ACGTcount: A:0.16, C:0.41, G:0.25, T:0.18
Consensus pattern (15 bp):
TATCCCCGACCGGCG
Found at i:318537 original size:30 final size:30
Alignment explanation
Indices: 318501--318571 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
318491 TATGCTTGGA
318501 ATGGGATATCCCCGACCGGCGTATCCCGCG
1 ATGGGATATCCCCGACCGGCGTATCCCGCG
318531 ATGGGATATCCCCGACCGGCGTATCCCGCG
1 ATGGGATATCCCCGACCGGCGTATCCCGCG
318561 ATGGGATATCC
1 ATGGGATATCC
318572 TCCAGCCGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.18, C:0.34, G:0.30, T:0.18
Consensus pattern (30 bp):
ATGGGATATCCCCGACCGGCGTATCCCGCG
Found at i:318570 original size:15 final size:14
Alignment explanation
Indices: 318501--318571 Score: 56
Period size: 15 Copynumber: 4.8 Consensus size: 14
318491 TATGCTTGGA
318501 ATGGGATATCCCCG
1 ATGGGATATCCCCG
*
318515 ACCGGCG-TATCCCGCG
1 A-TGG-GATATCCC-CG
318531 ATGGGATATCCCCG
1 ATGGGATATCCCCG
*
318545 ACCGGCG-TATCCCGCG
1 A-TGG-GATATCCC-CG
318561 ATGGGATATCC
1 ATGGGATATCC
318572 TCCAGCCGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 15
0.70 0.06 0.23
Matches are distributed among these distances:
14 6 0.13
15 31 0.69
16 8 0.18
ACGTcount: A:0.18, C:0.34, G:0.30, T:0.18
Consensus pattern (14 bp):
ATGGGATATCCCCG
Found at i:327741 original size:34 final size:34
Alignment explanation
Indices: 327689--327760 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
327679 TTTAAATTAA
* * *
327689 AAAATTTATATTACATTAGTG-ATGAGTAGTTATG
1 AAAAGTTATACTACATTAG-GAATGAGTAATTATG
* *
327723 AAAAGTTATACTATATTAGGAATTAGTAATTATG
1 AAAAGTTATACTACATTAGGAATGAGTAATTATG
327757 AAAA
1 AAAA
327761 TGATTAGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 1 0.03
34 31 0.97
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.38
Consensus pattern (34 bp):
AAAAGTTATACTACATTAGGAATGAGTAATTATG
Found at i:328399 original size:34 final size:30
Alignment explanation
Indices: 328360--328422 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
328350 CAAAAATTAA
*
328360 TAAAATTTTAAGTATATATTTTATAATTAAATTT
1 TAAAATTTT-ACTAT-TA-TTTA-AATTAAATTT
328394 TAAAATTTTACTATTATTTAAATTAAATT
1 TAAAATTTTACTATTATTTAAATTAAATT
328423 CAGAGCAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 9 0.32
31 4 0.14
32 2 0.07
33 4 0.14
34 9 0.32
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
TAAAATTTTACTATTATTTAAATTAAATTT
Found at i:330986 original size:148 final size:148
Alignment explanation
Indices: 330718--331013 Score: 583
Period size: 148 Copynumber: 2.0 Consensus size: 148
330708 ATTAATAATA
330718 TATATTAATTTTATTTGTAGTTTTTTCTCCAAACAATCCCGCGATTACGGGTTGTTTTTTTGGTT
1 TATATTAATTTTATTTGTAGTTTTTTCTCCAAACAATCCCGCGATTACGGGTTGTTTTTTTGGTT
330783 TCTTTCAATCGCCCGCTCGCAAATCCATCGTCTCGATCCAATCCCAGAAACGTCCACTTTTTTCT
66 TCTTTCAATCGCCCGCTCGCAAATCCATCGTCTCGATCCAATCCCAGAAACGTCCACTTTTTTCT
330848 TGAGCTTTCTTTTCGAAT
131 TGAGCTTTCTTTTCGAAT
*
330866 TATATTAATTTTATTTGTATTTTTTTCTCCAAACAATCCCGCGATTACGGGTTGTTTTTTTGGTT
1 TATATTAATTTTATTTGTAGTTTTTTCTCCAAACAATCCCGCGATTACGGGTTGTTTTTTTGGTT
330931 TCTTTCAATCGCCCGCTCGCAAATCCATCGTCTCGATCCAATCCCAGAAACGTCCACTTTTTTCT
66 TCTTTCAATCGCCCGCTCGCAAATCCATCGTCTCGATCCAATCCCAGAAACGTCCACTTTTTTCT
330996 TGAGCTTTCTTTTCGAAT
131 TGAGCTTTCTTTTCGAAT
331014 CCGTACCGTT
Statistics
Matches: 147, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 147 1.00
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.42
Consensus pattern (148 bp):
TATATTAATTTTATTTGTAGTTTTTTCTCCAAACAATCCCGCGATTACGGGTTGTTTTTTTGGTT
TCTTTCAATCGCCCGCTCGCAAATCCATCGTCTCGATCCAATCCCAGAAACGTCCACTTTTTTCT
TGAGCTTTCTTTTCGAAT
Found at i:344668 original size:15 final size:14
Alignment explanation
Indices: 344650--344683 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
344640 AGAGGAAAGG
344650 GAGAGGGAAAGAGAA
1 GAGAGGGAAAGAG-A
344665 GAGAGGGAAAGAGA
1 GAGAGGGAAAGAGA
344679 GAGAG
1 GAGAG
344684 AAAGAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (14 bp):
GAGAGGGAAAGAGA
Found at i:344673 original size:27 final size:27
Alignment explanation
Indices: 344635--344690 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
344625 AAGGCGGAGG
* *
344635 GAAGAAGAGGAAAGGGAGAGGGAAAGA
1 GAAGAAGAGGAAAGAGAGAGAGAAAGA
344662 GAAG-AGAGGGAAAGAGAGAGAGAAAGA
1 GAAGAAGA-GGAAAGAGAGAGAGAAAGA
344689 GA
1 GA
344691 TTTCAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (27 bp):
GAAGAAGAGGAAAGAGAGAGAGAAAGA
Found at i:344688 original size:12 final size:12
Alignment explanation
Indices: 344636--344690 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
344626 AGGCGGAGGG
344636 AAGA-AGAG-GA
1 AAGAGAGAGAGA
* *
344646 AAGGGAGAGGGA
1 AAGAGAGAGAGA
344658 AAGAGAAGAGAGGGA
1 AAGAG-AGAGA--GA
344673 AAGAGAGAGAGA
1 AAGAGAGAGAGA
344685 AAGAGA
1 AAGAGA
344691 TTTCAATGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 3 0.08
11 4 0.11
12 14 0.38
13 4 0.11
14 5 0.14
15 7 0.19
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (12 bp):
AAGAGAGAGAGA
Found at i:357736 original size:15 final size:16
Alignment explanation
Indices: 357706--357744 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
357696 TGATAAATAT
357706 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
357723 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
357738 ATAATTT
1 ATAATTT
357745 TTTAAATGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:379798 original size:60 final size:60
Alignment explanation
Indices: 379734--379858 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
379724 TCAAGTTTAG
* * * * *
379734 GTACCTAATCGAGCCAAAA-TAAACTTTAGGTATCAAATTAAACCTTAAAGCCAATTTCAA
1 GTACCTAAT-GAGACAAAAGAAAACTTTAGGTACCAAATTAAACCTTAAAGCCAAATACAA
* * * *
379794 GTACCTAATTAGACAAAAGAAAATTTTAGGTACCAATTTAAACTTTAAAGCCAAATACAA
1 GTACCTAATGAGACAAAAGAAAACTTTAGGTACCAAATTAAACCTTAAAGCCAAATACAA
379854 GTACC
1 GTACC
379859 AAAATGTATA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 7 0.13
60 48 0.87
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.26
Consensus pattern (60 bp):
GTACCTAATGAGACAAAAGAAAACTTTAGGTACCAAATTAAACCTTAAAGCCAAATACAA
Found at i:382647 original size:18 final size:19
Alignment explanation
Indices: 382624--382659 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
382614 TTTTCCTAGA
382624 TAAAAGTATTA-GGATAGG
1 TAAAAGTATTAGGGATAGG
382642 TAAAAGTATTAGGGATAG
1 TAAAAGTATTAGGGATAG
382660 AGATAGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (19 bp):
TAAAAGTATTAGGGATAGG
Found at i:410755 original size:9 final size:9
Alignment explanation
Indices: 410743--410810 Score: 50
Period size: 9 Copynumber: 7.2 Consensus size: 9
410733 AAATATATTT
410743 ATTTTTTAA
1 ATTTTTTAA
*
410752 ATTTTTTTA
1 ATTTTTTAA
410761 ATTTTTT-A
1 ATTTTTTAA
*
410769 A-TTTTAAA
1 ATTTTTTAA
410777 ATATTTTTAAAA
1 AT-TTTTT--AA
410789 TACTTTTTTAA
1 -A-TTTTTTAA
*
410800 ATTTTTAAA
1 ATTTTTTAA
410809 AT
1 AT
410811 AAATTTTTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
7 4 0.08
8 4 0.08
9 24 0.50
10 5 0.10
11 2 0.04
12 2 0.04
13 6 0.12
14 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:410801 original size:12 final size:11
Alignment explanation
Indices: 410770--410811 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
410760 AATTTTTTAA
410770 TTTTAAAATAT
1 TTTTAAAATAT
410781 TTTTAAAATACT
1 TTTTAAAATA-T
*
410793 TTTT-TAA-AT
1 TTTTAAAATAT
410802 TTTTAAAATA
1 TTTTAAAATA
410812 AATTTTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 5 0.19
10 3 0.12
11 13 0.50
12 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:410817 original size:21 final size:21
Alignment explanation
Indices: 410779--410818 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
410769 ATTTTAAAAT
**
410779 ATTTTTAAAATACTTTTTTAA
1 ATTTTTAAAATAAATTTTTAA
410800 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
410819 GGTGTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTAA
Found at i:410876 original size:16 final size:16
Alignment explanation
Indices: 410839--410877 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
410829 AAAAAATAGG
410839 CGGCCCAAACTCGGCC
1 CGGCCCAAACTCGGCC
* *
410855 CAGCCCAAATTCGGCC
1 CGGCCCAAACTCGGCC
*
410871 TGGCCCA
1 CGGCCCA
410878 GCCCATGAGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.21, C:0.46, G:0.23, T:0.10
Consensus pattern (16 bp):
CGGCCCAAACTCGGCC
Found at i:411359 original size:21 final size:20
Alignment explanation
Indices: 411333--411397 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 20
411323 GTGTATCTTA
*
411333 TTTTAACATACAAAGACTATT
1 TTTTAACATA-AAAGACTAAT
*
411354 TTTTAACAATAAAAATGAATAAT
1 TTTTAAC-AT-AAAA-GACTAAT
411377 TTTTAACA-AAAAGACTAAT
1 TTTTAACATAAAAGACTAAT
411396 TT
1 TT
411398 GATCTTTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 8 0.21
20 4 0.11
21 7 0.18
22 6 0.16
23 13 0.34
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (20 bp):
TTTTAACATAAAAGACTAAT
Found at i:418744 original size:16 final size:16
Alignment explanation
Indices: 418725--418755 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
418715 AATCATTCGA
418725 TTTGAATATTATTAAG
1 TTTGAATATTATTAAG
*
418741 TTTGAATTTTATTAA
1 TTTGAATATTATTAA
418756 TTCGATCAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (16 bp):
TTTGAATATTATTAAG
Found at i:419677 original size:20 final size:21
Alignment explanation
Indices: 419652--419691 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
419642 CGAGTGCATG
419652 AAAATCCAAAAAT-TTAATAT
1 AAAATCCAAAAATATTAATAT
* *
419672 AAAATCTAATAATATTAATA
1 AAAATCCAAAAATATTAATA
419692 CACACAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATCCAAAAATATTAATAT
Found at i:425931 original size:22 final size:21
Alignment explanation
Indices: 425901--425941 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
425891 TTTTGTGAAC
*
425901 TTTTTATATGTTTTAATTTTTA
1 TTTTGATAT-TTTTAATTTTTA
*
425923 TTTTGATATTTTTTATTTT
1 TTTTGATATTTTTAATTTT
425942 CATAATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTTGATATTTTTAATTTTTA
Found at i:425935 original size:15 final size:15
Alignment explanation
Indices: 425914--425952 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
425904 TTATATGTTT
*
425914 TAATTTTTATTTTGA
1 TAATTTTTATTTTCA
*
425929 TATTTTTTATTTTCA
1 TAATTTTTATTTTCA
425944 TAATTTTTA
1 TAATTTTTA
425953 AATTATTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (15 bp):
TAATTTTTATTTTCA
Found at i:427285 original size:25 final size:25
Alignment explanation
Indices: 427234--427287 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
427224 TCATTATGCC
** *
427234 AATTTTAAATAAAAATAGTTTTGAA
1 AATTTTAAATAAAAATAAATATGAA
427259 AATTTTAAATAAAAATTAAATAT-AA
1 AATTTTAAATAAAAA-TAAATATGAA
427284 AATT
1 AATT
427288 ATAGGGCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
AATTTTAAATAAAAATAAATATGAA
Found at i:432692 original size:22 final size:22
Alignment explanation
Indices: 432658--432701 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
432648 TTAACAACTT
*
432658 AATGACTTAAATAAATTTTTTTA
1 AATGACTTAAAT-AATTATTTTA
*
432681 AATGA-TTTAATAATTATTTTA
1 AATGACTTAAATAATTATTTTA
432702 TAATTTTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 5 0.26
23 5 0.26
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
AATGACTTAAATAATTATTTTA
Found at i:439948 original size:23 final size:22
Alignment explanation
Indices: 439902--439948 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
439892 TTTCTTTCAA
* **
439902 TTGTTTTTTTTGGTGATATTGT
1 TTGTTTTTTTTGGTGAGAAAGT
439924 TTGTTTTTTTTGGTTGAGAAAGT
1 TTGTTTTTTTTGG-TGAGAAAGT
439947 TT
1 TT
439949 TGATATTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.13, C:0.00, G:0.23, T:0.64
Consensus pattern (22 bp):
TTGTTTTTTTTGGTGAGAAAGT
Found at i:447419 original size:14 final size:14
Alignment explanation
Indices: 447394--447421 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
447384 AATTATTTTC
447394 TTACAAATATTATG
1 TTACAAATATTATG
447408 TTACAAATATTATG
1 TTACAAATATTATG
447422 AGGGCACGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TTACAAATATTATG
Found at i:447726 original size:14 final size:14
Alignment explanation
Indices: 447701--447728 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
447691 AATTATTTTC
447701 TTACAAATATTATG
1 TTACAAATATTATG
447715 TTACAAATATTATG
1 TTACAAATATTATG
447729 AGGGCACGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TTACAAATATTATG
Found at i:447846 original size:307 final size:308
Alignment explanation
Indices: 447279--447895 Score: 1227
Period size: 307 Copynumber: 2.0 Consensus size: 308
447269 AAAATTAGGG
447279 GTTTTTAAAGATAAAAATTATAAGTTATATAAGAGGTTTTCTGAACATTAATATATTGGCTCGGA
1 GTTTTTAAAGATAAAAATTATAAGTTATATAAGAGGTTTTCTGAACATTAATATATTGGCTCGGA
447344 GTGGATTTTAACACTATTCATTTGCTTAAATTTTTTTATAAATTATTTTCTTACAAATATTATGT
66 GTGGATTTTAACACTATTCATTTGCTTAAATTTTTTTATAAATTATTTTCTTACAAATATTATGT
447409 TACAAATATTATGAGGGCACGTTGTAAAAAAAACGTGGCTTTTACAAATTGTATATACTTTAAAC
131 TACAAATATTATGAGGGCACGTTGTAAAAAAAACGTGGCTTTTACAAATTGTATATACTTTAAAC
447474 AACATCGTTAAATTTATTAAGTTCTACTATTTTCAAAATATTATGTGTTAAATATATTATCAGAT
196 AACATCGTTAAATTTATTAAGTTCTACTATTTTCAAAATATTATGTGTTAAATATATTATCAGAT
447539 GTGTAATGCTATGTCAAATTTCTATTTGTACATATTACTCACAAAAAT
261 GTGTAATGCTATGTCAAATTTCTATTTGTACATATTACTCACAAAAAT
447587 GTTTTTAAAGAT-AAAATTATAAGTTATATAAGAGGTTTTCTGAACATTAATATATTGGCTCGGA
1 GTTTTTAAAGATAAAAATTATAAGTTATATAAGAGGTTTTCTGAACATTAATATATTGGCTCGGA
447651 GTGGATTTTAACACTATTCATTTGCTTAAATTTTTTTATAAATTATTTTCTTACAAATATTATGT
66 GTGGATTTTAACACTATTCATTTGCTTAAATTTTTTTATAAATTATTTTCTTACAAATATTATGT
447716 TACAAATATTATGAGGGCACGTTGTAAAAAAAACGTGGCTTTTACAAATTGTATATACTTTAAAC
131 TACAAATATTATGAGGGCACGTTGTAAAAAAAACGTGGCTTTTACAAATTGTATATACTTTAAAC
447781 AACATCGTTAAATTTATTAAGTTCTACTATTTTCAAAATATTATGTGTTAAATATATTATCAGAT
196 AACATCGTTAAATTTATTAAGTTCTACTATTTTCAAAATATTATGTGTTAAATATATTATCAGAT
447846 GTGTAATGCTATGTCAAATTTCTATTTGTACATATTACTCACAAAAAT
261 GTGTAATGCTATGTCAAATTTCTATTTGTACATATTACTCACAAAAAT
447894 GT
1 GT
447896 CAGTTGATGG
Statistics
Matches: 309, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
307 297 0.96
308 12 0.04
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (308 bp):
GTTTTTAAAGATAAAAATTATAAGTTATATAAGAGGTTTTCTGAACATTAATATATTGGCTCGGA
GTGGATTTTAACACTATTCATTTGCTTAAATTTTTTTATAAATTATTTTCTTACAAATATTATGT
TACAAATATTATGAGGGCACGTTGTAAAAAAAACGTGGCTTTTACAAATTGTATATACTTTAAAC
AACATCGTTAAATTTATTAAGTTCTACTATTTTCAAAATATTATGTGTTAAATATATTATCAGAT
GTGTAATGCTATGTCAAATTTCTATTTGTACATATTACTCACAAAAAT
Found at i:458669 original size:20 final size:20
Alignment explanation
Indices: 458630--458671 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
458620 ATGTTAGAGT
*
458630 TAATATAGTCAAAGCAGTTG
1 TAATATAGTCAAAACAGTTG
*
458650 TAATATAGTCAAAACTGTTG
1 TAATATAGTCAAAACAGTTG
458670 TA
1 TA
458672 CCGTTGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
TAATATAGTCAAAACAGTTG
Found at i:458700 original size:15 final size:15
Alignment explanation
Indices: 458680--458710 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
458670 TACCGTTGTA
458680 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
458695 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
458710 A
1 A
458711 AAGATGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (15 bp):
AGTCTGTTAGCAGTT
Found at i:463981 original size:20 final size:20
Alignment explanation
Indices: 463942--463983 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
463932 ATGTTAGAGT
*
463942 TAATATAGTCAAAGCAGTTG
1 TAATATAGTCAAAACAGTTG
*
463962 TAATATAGTCAAAACTGTTG
1 TAATATAGTCAAAACAGTTG
463982 TA
1 TA
463984 CCGTTGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
TAATATAGTCAAAACAGTTG
Found at i:464012 original size:15 final size:15
Alignment explanation
Indices: 463992--464022 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
463982 TACCGTTGTA
463992 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
464007 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
464022 A
1 A
464023 AAGATGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (15 bp):
AGTCTGTTAGCAGTT
Found at i:471397 original size:9 final size:9
Alignment explanation
Indices: 471383--471414 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
471373 AACTTGGTGC
471383 ATTTTGTTT
1 ATTTTGTTT
471392 ATTTTGTTT
1 ATTTTGTTT
471401 ATTTTGTTT
1 ATTTTGTTT
471410 ATTTT
1 ATTTT
471415 TAATATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:471495 original size:23 final size:23
Alignment explanation
Indices: 471465--471516 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
471455 TGCAACTTGG
471465 TTTCATAATAATAGCTA-ATATGC
1 TTTCATAATAATAGCTATA-ATGC
*
471488 TTTCATAATGATAGCTATAATGC
1 TTTCATAATAATAGCTATAATGC
471511 TTTCAT
1 TTTCAT
471517 CTTTTGCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (23 bp):
TTTCATAATAATAGCTATAATGC
Found at i:471528 original size:59 final size:59
Alignment explanation
Indices: 471465--471580 Score: 196
Period size: 59 Copynumber: 2.0 Consensus size: 59
471455 TGCAACTTGG
*
471465 TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTATAATGCTTTCATCTTTTGC
1 TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTACAATGCTTTCATCTTTTGC
* * *
471524 TTTCATAATGATAGCTAATATGCTTTCATAATGGTAGTTACAATGCTTTCATCTTTT
1 TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTACAATGCTTTCATCTTTT
471581 TAATTATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (59 bp):
TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTACAATGCTTTCATCTTTTGC
Found at i:471549 original size:23 final size:23
Alignment explanation
Indices: 471521--471575 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
471511 TTTCATCTTT
471521 TGCTTTCATAATGATAGCTA-ATA
1 TGCTTTCATAATGATAGCTACA-A
* *
471544 TGCTTTCATAATGGTAGTTACAA
1 TGCTTTCATAATGATAGCTACAA
471567 TGCTTTCAT
1 TGCTTTCAT
471576 CTTTTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (23 bp):
TGCTTTCATAATGATAGCTACAA
Found at i:480400 original size:44 final size:44
Alignment explanation
Indices: 480337--480425 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
480327 TGAAGATAAG
480337 TGGCATTGTAAAGAACGTTTACATTACGAGAAAGATAACTTACT
1 TGGCATTGTAAAGAACGTTTACATTACGAGAAAGATAACTTACT
480381 TGGCATTGTAAAGAACGTTTACATTACGAGAAAGATAACTTACT
1 TGGCATTGTAAAGAACGTTTACATTACGAGAAAGATAACTTACT
480425 T
1 T
480426 CAGTAGATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (44 bp):
TGGCATTGTAAAGAACGTTTACATTACGAGAAAGATAACTTACT
Found at i:489733 original size:22 final size:24
Alignment explanation
Indices: 489707--489750 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
489697 GAAAAATATT
489707 AAATAT-AT-ATTTTTTATTTTTA
1 AAATATAATAATTTTTTATTTTTA
489729 AAATATAATAATTTTTTATTTT
1 AAATATAATAATTTTTTATTTT
489751 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 2 0.10
24 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
AAATATAATAATTTTTTATTTTTA
Found at i:489880 original size:59 final size:59
Alignment explanation
Indices: 489817--489992 Score: 244
Period size: 68 Copynumber: 2.8 Consensus size: 59
489807 TCAAGTTTGT
*
489817 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
*
489876 TTTACTAATCAAATGTTAGATTTTATTACAAAAATTAATACAATTAATACAGTTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTAC--------A-ACAATTAATACAATTAATAATTTGAT
489941 AAA
57 AAA
*
489944 TTTACTAATCAAATGTTAGATTTTATTACAAAAATTAATACAATTAATA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATA
489993 CAGTTAATAA
Statistics
Matches: 104, Mismatches: 4, Indels: 18
0.83 0.03 0.14
Matches are distributed among these distances:
59 45 0.43
60 1 0.01
67 1 0.01
68 57 0.55
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:489924 original size:68 final size:68
Alignment explanation
Indices: 489847--490010 Score: 319
Period size: 68 Copynumber: 2.4 Consensus size: 68
489837 TTTTGTTACA
*
489847 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAAAAATT
1 ACAATTAATACAGTTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAAAAATT
489912 AAT
66 AAT
489915 ACAATTAATACAGTTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAAAAATT
1 ACAATTAATACAGTTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAAAAATT
489980 AAT
66 AAT
489983 ACAATTAATACAGTTAATAATTTGATAA
1 ACAATTAATACAGTTAATAATTTGATAA
490011 TAAACGGGCT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 95 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.39
Consensus pattern (68 bp):
ACAATTAATACAGTTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAAAAATT
AAT
Found at i:509953 original size:30 final size:30
Alignment explanation
Indices: 509917--509978 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
509907 AGGGGGAGGC
*
509917 GGCATTCCAGGGCGTGGGGGTGGTGGAGCA
1 GGCATTCCAGGGCGTGGGGGTGGTGGACCA
*
509947 GGCATTCCAGGGCGTGGTGGTGGTGGACCA
1 GGCATTCCAGGGCGTGGGGGTGGTGGACCA
509977 GG
1 GG
509979 AGGTCCTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.13, C:0.18, G:0.52, T:0.18
Consensus pattern (30 bp):
GGCATTCCAGGGCGTGGGGGTGGTGGACCA
Found at i:515061 original size:26 final size:27
Alignment explanation
Indices: 515023--515074 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
515013 AATGAGTAGA
* *
515023 TTTGAATACAAAAGA-AGAGAAAAAGC
1 TTTGAATAAAAAAAAGAGAGAAAAAGC
515049 TTTGAATAAAAAAAAGAGAGAAAAAG
1 TTTGAATAAAAAAAAGAGAGAAAAAG
515075 AGGTGATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.62, C:0.04, G:0.19, T:0.15
Consensus pattern (27 bp):
TTTGAATAAAAAAAAGAGAGAAAAAGC
Found at i:523408 original size:18 final size:19
Alignment explanation
Indices: 523374--523415 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
523364 ATCACATGTT
*
523374 TAAAATGAAAAT-TAAAAA
1 TAAAATGAAAATGAAAAAA
523392 TAAAAT-AAAATCGAAAAAA
1 TAAAATGAAAAT-GAAAAAA
523411 TAAAA
1 TAAAA
523416 ATGCGCTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 6 0.29
19 10 0.48
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (19 bp):
TAAAATGAAAATGAAAAAA
Found at i:524440 original size:18 final size:19
Alignment explanation
Indices: 524406--524447 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
524396 ATCACATGTT
*
524406 TAAAATGAAAAT-TAAAAA
1 TAAAATGAAAATGAAAAAA
524424 TAAAAT-AAAATCGAAAAAA
1 TAAAATGAAAAT-GAAAAAA
524443 TAAAA
1 TAAAA
524448 ATGCGCTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 6 0.29
19 10 0.48
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (19 bp):
TAAAATGAAAATGAAAAAA
Found at i:534970 original size:6 final size:6
Alignment explanation
Indices: 534959--534989 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
534949 TTTCACTTAG
534959 ATTTGT ATTTGT ATTTGT ATTTGT ATTTGT A
1 ATTTGT ATTTGT ATTTGT ATTTGT ATTTGT A
534990 ATTTAACGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.65
Consensus pattern (6 bp):
ATTTGT
Found at i:538031 original size:3 final size:3
Alignment explanation
Indices: 538023--538051 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
538013 CCTAGTTGTT
538023 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
538052 TTTTCAGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:543190 original size:45 final size:45
Alignment explanation
Indices: 543139--543274 Score: 272
Period size: 45 Copynumber: 3.0 Consensus size: 45
543129 TTTTGCTCTT
543139 ATGCTTTGAATGATCATATATTTACCTACAGTTGATGATAAGACA
1 ATGCTTTGAATGATCATATATTTACCTACAGTTGATGATAAGACA
543184 ATGCTTTGAATGATCATATATTTACCTACAGTTGATGATAAGACA
1 ATGCTTTGAATGATCATATATTTACCTACAGTTGATGATAAGACA
543229 ATGCTTTGAATGATCATATATTTACCTACAGTTGATGATAAGACA
1 ATGCTTTGAATGATCATATATTTACCTACAGTTGATGATAAGACA
543274 A
1 A
543275 AAGAGGGCAT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 91 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (45 bp):
ATGCTTTGAATGATCATATATTTACCTACAGTTGATGATAAGACA
Found at i:548116 original size:6 final size:6
Alignment explanation
Indices: 548105--548130 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
548095 TTATAAATGA
548105 TAAAAT TAAAAT TAAAAT TAAAAT TA
1 TAAAAT TAAAAT TAAAAT TAAAAT TA
548131 GAAAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAAAT
Found at i:558666 original size:16 final size:17
Alignment explanation
Indices: 558641--558674 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
558631 GAAAATTTTT
558641 AATAAATAA-TTAATTC
1 AATAAATAATTTAATTC
*
558657 AATAATTAATTTAATTC
1 AATAAATAATTTAATTC
558674 A
1 A
558675 TGTGACAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAAATAATTTAATTC
Found at i:563797 original size:22 final size:21
Alignment explanation
Indices: 563769--563809 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
563759 AATTTAATTT
563769 TTTTCTTTTATGTTTTTTTAAC
1 TTTTCTTTT-TGTTTTTTTAAC
*
563791 TTTTCTTTTTTTTTTTTTA
1 TTTTCTTTTTGTTTTTTTA
563810 TTTTCCATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.10, C:0.07, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTCTTTTTGTTTTTTTAAC
Found at i:580706 original size:30 final size:30
Alignment explanation
Indices: 580672--580757 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
580662 CTCCTTATAT
*
580672 CTATCTCTATGCCTACT-CCTATCTCTGCCC
1 CTATCTCTATCCCTA-TGCCTATCTCTGCCC
580702 CTATCTCTATCCCTATGCCTATCTCTGTCCC
1 CTATCTCTATCCCTATGCCTATCTCTG-CCC
* *
580733 TCTTATCCCTATCCCTATCCCTATC
1 -C-TATCTCTATCCCTATGCCTATC
580758 CCTATCCTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
29 1 0.02
30 24 0.49
31 3 0.06
32 1 0.02
33 20 0.41
ACGTcount: A:0.14, C:0.43, G:0.05, T:0.38
Consensus pattern (30 bp):
CTATCTCTATCCCTATGCCTATCTCTGCCC
Done.